What’s wrong with this paper?

Taking a new tack with the common descent/common design theme, I’d like to sneak up on it. As Sal Cordova likes to do, I offer a hypothesis for critique. Here’s an old phyogenetic analysis of mine. Does it show common descent? If not, what’s wrong with it?

Harshman J., Huddleston C.J., Bollback J., Parsons T.M., Braun M.J. True and false gharials: A nuclear gene phylogeny of Crocodylia. Systematic Biology 2003;  52:386-402.

This one is about crocodiles. Are crocodiles all the same kind? How do you know? If they aren’t how many kinds are there within the group and how do you know? If they are, are they a whole kind or just part of a larger kind? And if the latter, what is the larger kind?

216 thoughts on “What’s wrong with this paper?

  1. Thank you John for raising an interesting issue of kinds in relation to common descent…

    As some readers may know, I have been curious about the possibility of evolution within kinds after the Noah’s Flood…
    However, I have never gotten a clear-cut answer about the definition of KINDS from creationists and others…

    This could possibly be a good opportunity to clarify it… If not, perhaps a separate OP could deal with this… Maybe VJ. Torley is interested…

  2. I think its useful and fun to debate and discuss topics that there’s disagreement about. But I think that between people that accept science and creationists the gulf is so great that there can’t be a productive discussion. There’s no point in discussing species vs. ‘kinds’ until we can agree on our most basic ways of discerning reality. Should we interpret the natural world through a literal reading of the story of Noah’s Ark or is there a better way?

  3. What’s wrong is that you cherry-picked!!! (I’m just guessing Salvador’s answer to save time.)

  4. Entropy: What’s wrong is that you cherry-picked!!! (I’m just guessing Salvador’s answer to save time.)

    Why would Sal care about crocodiles?

  5. RodW,

    RodW: Should we interpret the natural world through a literal reading of the story of Noah’s Ark or is there a better way?

    We can interpret the natural world through abiogenesis that there is no shred of evidence for… Or through mutation breeding, the natural selection with a very strong element of randomness… or non-random mutations…
    What’s you pick?

  6. RodW: discussing species vs. ‘kinds’ until we can agree on our most basic ways of discerning reality.

    We could also discuss the “reality” of time… especially if particles or something can travel faster than the speed of light… then the age of the universe and the earth would need adjusting… just mildly put… 😉

  7. The phylogeny of Crocodylia offers an unusual twist on the usual molecules versus morphology story. The true gharial (Gavialis gangeticus) and the false gharial (Tomistoma schlegelii), as their common names imply, have appeared in all cladistic morphological analyses as distantly related species, convergent upon a similar morphology. In contrast, all previous molecular studies have shown them to be sister taxa.

    I’m going to quote-mine the paper and ask Rumraket what is wrong with my quote-mine. What twin nested hierarchy? What on earth does “the usual molecules versus morphology story” refer to?

  8. Mung: What on earth does “the usual molecules versus morphology story” refer to?

    The fact that there are a number of cases where a phylogeny that was derived from DNA or protein comparisons differs from the older way of doing it based on anatomical comparisons.

  9. J-Mac: We could also discuss the “reality” of time

    I think that time is real. What do you think? What is your reason for thinking that some particles go faster than light? (I’m not sure what physicists would say about this now) How would particles going faster than light change our estimate for the age of the universe? (isn’t the speed of light the only relevant speed?) but the most important question: what is your reason for thinking the current estimate for the age of the universe is wrong?

  10. Mung,

    as their common names imply, have appeared in all cladistic morphological analyses as distantly related species,

    Are there details available why the morphological analyses has them categorized this way. Is there any idea what genetically could be driving this difference?

  11. Mung: I’m…. wrong with my quote-mine.

    Mung, I’m pleased to see that you’ve finally admitted that you quote mine and that its wrong to do so.

  12. If nested hierarchy is falsified, so is evolution… So, it has to be defended at any cost…
    Carnivorous plants certainly falsify nested hierarchy having supposedly independently evolved tens of separated features in different species of the plant…

    Bladderwort trap is the gem with the door closing mechanism approaching the speed of light…

    https://www.youtube.com/watch?v=Zb_SLZFsMyQ

  13. Looks like one of the best papers I’ve seen in evolutionary biology. The thoroughness is amazing in examining the independent lines of evidence. It’s a model paper worth learning from.

    I have no opinion on the common design and common descent issue regarding these groups at this time.

  14. RodW: I think that time is real. What do you think

    I have my doubts about time in some sense but so did Einstein… So I’m not alone…

    Some experiments suggested that neutrinos outrun photons… now doomed as an error but entanglement seems to violate that premise…

    I’m not saying the estimated age of the universe is wrong but there are many variables it is based on that could be wrong… it’s a broad subject based on the premise that big bang happened that the universe had a beginning…

    The implications of something traveling faster than light would be enormous that would have to change the foundations of what we know about the laws of physics and the universe… Read up on that… it’s beyond the scope of this OP or this blog…

    BTW: There are speculations (Sal has his) that the earth, while being millions of billions years old, as per big bang estimates, that the actual appearance of life on earth could have happened millions of years later, after the earth was transformed for habitation over long periods of time…

  15. stcordova,

    They look like day and night to my unbiased eye… or like a plane and a submarine…. I’m sure internally they are very similar… just like plane and submarine having wires, electric circuits which prove common descent…

  16. Mung,

    Consequences for character evolution if the morphologicaltree is wrong.—Assuming that the molecular tree is cor-rect, what could be causing the morphological data tobe misleading? Gavialis must undergo a great many re-versals to the primitive condition, with postcranial char-acters disproportionately represented, from that sharedamong various more or less inclusive groups rangingfrom all other Crocodylia to all other Longirostres. Wehave no explanation for this pattern, but it deservesinvestigation

    True and False Gharials: A Nuclear Gene Phylogeny of Crocodylia (PDF Download Available). Available from: https://www.researchgate.net/publication/10734528_True_and_False_Gharials_A_Nuclear_Gene_Phylogeny_of_Crocodylia [accessed Dec 19 2017].

    There is no explanation for the difference in the morphological and genetic data. The paper was completed in 2003 has anyone picked up this ball since and made any progress?

  17. Here is a c-myc comparison, I see only 1 amino acid difference, a valine vs. an alanine in about position 21 or so. The introns may change between genes. But these are scored 100% coverage and 99.4% identity.


    Query 1 EEQEEDEEEIDVVTLVEVNGVESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPI 60
    EEQEEDEEEIDVVTLVEVNG ESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPI
    Sbjct 1 EEQEEDEEEIDVVTLVEVNGAESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPI 60

    Query 61 HQHNYAAPPSTKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLER 120
    HQHNYAAPPSTKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLER
    Sbjct 61 HQHNYAAPPSTKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLER 120

    Query 121 QRRNELKLSFFALRDEIPEVANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRR 180
    QRRNELKLSFFALRDEIPEVANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRR
    Sbjct 121 QRRNELKLSFFALRDEIPEVANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRR 180

    Query 181 DQLKHKLEQLRNSCA 195
    DQLKHKLEQLRNSCA
    Sbjct 181 DQLKHKLEQLRNSCA 195

    Here are the fasta sequences I used for a blastp. For completeness we should look at the genes.

    >tr|Q7T243|Q7T243_TOMSC C-myc (Fragment) OS=Tomistoma schlegelii GN=c-Myc PE=4 SV=1
    EEQEEDEEEIDVVTLVEVNGVESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPIHQHNYAAPPS
    TKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLERQRRNELKLSFFALRDEIPEV
    ANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRRDQLKHKLEQLRNSCA

    >tr|Q7T242|Q7T242_GAVGA C-myc (Fragment) OS=Gavialis gangeticus GN=c-Myc PE=4 SV=1
    EEQEEDEEEIDVVTLVEVNGAESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPIHQHNYAAPPS
    TKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLERQRRNELKLSFFALRDEIPEV
    ANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRRDQLKHKLEQLRNSCA

  18. This is the protein sequence that bears John Harshman’s name as author for the “false” gharials.

    Excellent work, btw:

    https://www.ncbi.nlm.nih.gov/protein/AAP41723.1?report=genbank&log$=prottop&blast_rank=1&RID=3JKG3823013

    AAP41723.1

    AUTHORS Harshman,J., Huddleston,C.J., Bollback,J.P., Parsons,T.J. and
    Braun,M.J.

    eeqeedeeei dvvtlvevng vesgtesstd ssgesstdst dghskphhsp lvlkrchvpi
    hqhnyaapps tkveypsakr lkldngrilk qisnnrkcss prtsdseend krrthnvler
    qrrnelklsf falrdeipev annekapkvv ilkkateyvi siqadehrli aekeqlrrrr
    dqlkhkleql rnsca

  19. colewd,

    “…All studies of mitochondrial DNA (mtDNA) sequencedata (Gatesy and Amato, 1992; Gatesy et al., 1993;Aggarwal et al., 1994; Poe, 1996; White and Densmore,2001, unpubl.) have included outgroups, and all havesupported the molecular tree. However, one of Whiteand Densmore’s (unpubl.) analyses produced a differentresult (root 4, Fig. 1c). Rooting is a difficulty in molecularanalyses, because the closest extant outgroup, birds, is extremely distant from the ingroup; thus, the branchconnecting the ingroup and the outgroup is very long.It might be argued that mtDNA sequences retain rela-tively little phylogenetic signal at such high divergences.Gatesy et al.’s (2003) ”

    Some studies produced different results though…

  20. I posted to the wrong thread. Apologies.

    This is the gene (the previous comment was for the protein) for the “false” gharial that bears John’s name as author. Excellent work again.

    https://www.ncbi.nlm.nih.gov/nuccore/AY277487.1

    >AY277487.1 Crocodylus cataphractus c-myc (c-Myc) gene, exon 3 and partial cds
    GCAGCATGGGGGGGGGCGGACACGGGAGGGTGCTGTCACATCTGTCAGCAGTCGACTTCCCTGCTCTCTG
    GGCACTTAGGCAAGATCTCTAACGAGATCAAGAGATCTGGGGCGCAGGGCTTAGCCCTGAGGGGAGGCGG
    ATGTTCAAGCCGTGGGCAGGAGCATCCTGTTGCATGCTGGATGCTAGATTTCTGGGAGGAAATAGTTTTT
    GGGGAAGTGCAGGTTTTTGAAGCCAATTACAACATGTTTAAAATTCAGTTTGCCGCTGTTCTTCCAAGCC
    CAGAATAAGGTCCTGTTTTGAAACCCGGGGCTTCTTTAAATCTACAAATTAACTGTTTTTTCTTTTTCTT
    GCAGAAGAAGAACAAGAGGAAGATGAGGAGGAAATTGATGTGGTCACGCTAGTAGAGGTGAATGGAGTTG
    AATCCGGCACAGAGTCTAGTACAGACTCTAGCGGAGAGTCTAGCACAGATTCCACAGACGGACACAGCAA
    GCCACACCACAGCCCGCTAGTTCTCAAGCGGTGTCATGTCCCCATCCATCAGCACAATTACGCTGCTCCT
    CCTTCCACCAAGGTTGAATATCCGTCAGCAAAGAGGTTAAAATTGGACAATGGCAGGATTCTCAAGCAGA
    TCAGTAACAACAGAAAGTGCTCAAGTCCCCGCACATCAGACTCGGAAGAAAACGACAAGAGGCGAACGCA
    CAACGTCCTGGAGCGCCAAAGGAGAAACGAGCTGAAGTTGAGCTTCTTTGCTTTGCGTGACGAGATACCC
    GAGGTAGCCAACAATGAAAAGGCGCCCAAAGTCGTCATCCTTAAAAAAGCAACGGAATATGTTATTTCTA
    TTCAAGCAGATGAGCACAGACTGATAGCAGAGAAAGAGCAGCTGAGGAGGCGGCGAGATCAATTGAAACA
    CAAACTTGAGCAGCTAAGGAACTCTTGTGCATAGAAACTCTTGGGTATAGACTTGAGTAACCCAAACCAG
    GCTGAAATATGATAAAAAATATTAATGTTTCTAATCTTACTCATGACCTACACCGGTTCCAAAAGGAGCT
    CTTGCAATTGCATGCTGTGCGGAATGACTTGCAACTACACAACCTTGGCTTTGTCTCTCGAGCTGAGCCA
    TAACCTCAAC

  21. I posted earlier to the wrong thread (common descent vs. common design). Here it is.

    This is the gene that is of the TRUE gharial. It also bears John Harshman’s name as author. Excellent work again.

    https://www.ncbi.nlm.nih.gov/nucleotide/AY277488.1?report=genbank&log$=nucltop&blast_rank=2&RID=3JMRMT8A013

    >AY277488.1 Osteolaemus tetraspis c-myc (c-Myc) gene, exon 3 and partial cds
    GCAGCATGGGGGGGGGCRGACACGGGAGGGTGCTGTCACATCTGTCAGCAGTCGACTTCCCTGCTCTCTG
    GGCACTTAGGCAAGATCTCTAACGAGATCAAGAGATCTGGGGCGCAGGGCTTAGCCCTGAGGGGAGGCGG
    ATGTTCAAGCCGTGGGCAGGAGCATCCTGTTGCATGCTGGATGCTAGATTTCTGGGAGGAAATAGTTTTT
    GGGGAAGTGCAGGTTTTTGAAGCCAATTACAACATGTTTAAAATTCAGTTTGCCGCTGTTCTTCCAAGCC
    CAGAATAAGGTCCTGTTTTGAAACCCGGGGCTTCTTTAAATCTACAAATTAACTGTTTTTTCTTTTTCTT
    GCAGAAGAAGAACAAGAGGAAGATGAGGAGGAAATTGATGTGGTCACGCTAGTAGAGGTGAATGGAGTTG
    AATCCGGCACAGAGTCTAGTACAGACTCTAGCGGAGAGTCTAGCACAGATTCCACAGACGGACACAGCAA
    GCCACACCACAGCCCGCTAGTTCTCAAGCGGTGTCATGTCCCCATCCATCAGCACAATTACGCTGCTCCT
    CCTTCCACCAAGGTTGAATATCCGTCAGCAAAGAGGTTAAAATTGGACAATGGCAGGATTCTCAAGCAGA
    TCAGTAACAACAGAAAGTGCTCAAGTCCCCGCACATCAGACTCGGAAGAAAACGACAAGAGGCGAACGCA
    CAACGTCCTGGAGCGCCAAAGGAGAAACGAGCTGAAGTTGAGCTTCTTTGCTTTGCGTGACGAGATACCC
    GAGGTAGCCAACAATGAAAAGGCGCCCAAAGTCGTCATCCTTAAAAAAGCAACGGAATATGTTATTTCTA
    TTCAAGCAGATGAGCACAGACTGATAGCAGAGAAAGAGCAGCTGAGGCGGCGGCGAGATCAATTGAAACA
    CAAACTTGAGCAGCTAAGGAACTCTTGTGCATAGAAACTCTTGGGTATAGACTTGAGTAACCCAAACCAG
    GCTGAAATATGATAAAAAATATTAATGTTTCTAATCTTACTCATGACCTACACCGGTTCCAAAAGGAGCT
    CTTGCAATTGCATGCTGTGCGGAATGACTTGCAACTACACAACCTTGGCTTTGTCTCTCGAGCTGAGCCA
    TAACCTCAAC

  22. J-Mac: BTW: There are speculations (Sal has his) that the earth, while being millions of billions years old, as per big bang estimates

    Since the Big Bang is thought to be about 13 billion years ago, perhaps this is a typo. General accepted number for solar system is around 4.5 billion

    that the actual appearance of life on earth could have happened millions of years later, after the earth was transformed for habitation over long periods of time…

    About 700 million years later is the present estimate. Modern human intelligence arrived around three billion seven hundred ninety-nine million eight hundred thousand years later. The universe took its time achieving its purpose.

    ETA: Sorry for the derail

  23. colewd: Are there details available why the morphological analyses has them categorized this way.

    There are some. Read the paper. You might also try Gatesy J., Amato G., Norell M., DeSalle R., Hayashi C. Combined support for wholesale taxic atavism in gavialine crocodylians. Systematic Biology 2003; 52:403-422.

    Is there any idea what genetically could be driving this difference?

    I don’t understand the question.

  24. stcordova:
    I posted to the wrong thread. Apologies.

    This is the gene (the previous comment was for the protein) for the “false” gharial that bears John’s name as author.Excellent work again.

    https://www.ncbi.nlm.nih.gov/nuccore/AY277487.1

    No, that’s the wrong species again. This time you have the African slender-snouted crocodile, Crocodylus cataphractus, which actually has a new name, Mecistops. How do you make this mistake twice in different ways?

  25. stcordova:
    I posted earlier to the wrong thread (common descent vs. common design).Here it is.

    This is the gene that is of the TRUE gharial.It also bears John Harshman’s name as author.Excellent work again.

    Why are you posting all these sequences? Is there a point? I must ask you not to use this thread as a notepad.

  26. Here is diagram highlighting what looks like a parital exon from c-myc from coordinates 355 to 1130 in the TRUE gharial. Since I don’t see the methionine codon (ATG) in this exon, I presume this is not the first exon, further I see the Intron acceptor sequence “ag” just before exon. Further I don’t see the donor site sequence “GT” for the subsequent intron. Do you concur, John?

    Is the reason we don’t have the whole gene to study, but instead got chopped off like that due to the sequencing technology involved? Anyway, excellent work.

    Click to enlarge image:
    http://theskepticalzone.com/wp/wp-content/uploads/2017/12/exon_diagram_true_gharial.png

  27. Why are you posting all these sequences? Is there a point?

    You want to discuss the paper don’t you and the data. I mean, this is about the data after all, isn’t it? I’m trying to make sure I got all the data properly referenced to examine. I’m double checking. Or would your rather make vague arguments rather than deal with the data your name is attached to.

    I’d think you’d be glad people are studying your paper. You want a critique of yoru data, you can get one. But you complain like that you won’t. Up to you, John, it’s your thread.

    Why are you posting all these sequences? Is there a point?

    Well, yes. I did have some critical question I wanted to ask and learn about. But since you took offense that I posted your laboratory work for examination, maybe I should just bail and continue in Noyau. It’s up to you.

  28. John Harshman:

    No, that’s the wrong species again. This time you have the African slender-snouted crocodile, Crocodylus cataphractus, which actually has a new name, Mecistops. How do you make this mistake twice in different ways?

    Well, that’s why I’m posting these sequences to make sure. But that sequence does have your name however as author does it not?

  29. John Harshman:

    How do you make this mistake twice in different ways?

    I put this sequence in BLASTP for the “False” gharial:

    >tr|Q7T243|Q7T243_TOMSC C-myc (Fragment) OS=Tomistoma schlegelii GN=c-Myc PE=4 SV=1
    EEQEEDEEEIDVVTLVEVNGVESGTESSTDSSGESSTDSTDGHSKPHHSPLVLKRCHVPIHQHNYAAPPS
    TKVEYPSAKRLKLDNGRILKQISNNRKCSSPRTSDSEENDKRRTHNVLERQRRNELKLSFFALRDEIPEV
    ANNEKAPKVVILKKATEYVISIQADEHRLIAEKEQLRRRRDQLKHKLEQLRNSCA

    Tomistoma schlegelii is nowhere to be found in the first few hits. I presumed it was renamed. What do you get when you put this in the BLASTP? Why don’t I get Tomistoma schlegelii in GenBank but I get it in UNIPROT?

  30. RodW: The fact that there are a number of cases where a phylogeny that was derived from DNA or protein comparisons differs from the older way of doing it based on anatomical comparisons.

    Yes, I know. But if I said that people would have a fit. So thanks.

    Now the question is, does Rumraket know?

  31. Mung: I’m going to quote-mine the paper and ask Rumraket what is wrong with my quote-mine. What twin nested hierarchy? What on earth does “the usual molecules versus morphology story” refer to?

    My answer is that you focusing on the uncertainty wrt the position of a single taxon can be very misleading if your intention is to argue that we can’t say there is good evidence for common descent.

    It is not that there is anything wrong with looking closely at the case of a phylogenetic ambiguity. After all if such cases are ignored, they can’t be resolved. And it is interesting in it’s own right to consider both why and where such ambiguities arise in phylogenetic analysis, and what they imply.

    As I have said many times before, there is a considerable difference between saying that we are very sure there is a single tree of life (a single nested hiearchy), versus saying that we know exactly where everything fits into that tree.

    So let me ask you in turn here Mung: Do you believe that the case of the ambiguity surrounding the phylogenetic position of the true vs false gharial implies that we cannot even argue rationally, that gharials and crocodiles share common descent?

  32. Mung: Now the question is, does Rumraket know?

    Oh I see, you didn’t even want to have a substantive discussion, this was just supposed to be some attempt to take brainless snipes at Rumraket. Apparently you intended to insinuate that I believed there were never any incongruities between different data sets. Enlighten me Mung, what is the significance of this particular case of an incongruity?

  33. Rumraket: Apparently you intended to insinuate that I believed there were never any incongruities between different data sets.

    So now, when I say that the twin-nested hierarchy is a myth, or when I ask which twin-nested hierarchy, you’ll not have to act all confused, you’ll know exactly what I am talking about.

    The molecular tree matches the morphological tree, except when it doesn’t.

  34. Here is a creationist essay that that guesses the “false” and true gharials are commonly descended from a created kind that was on Noah’s ark:

    https://answersingenesis.org/creation-science/baraminology/an-initial-estimate-toward-identifying-and-numbering-the-ark-turtle-and-crocodile-kinds/

    Below is a brief description of each estimated crocodylian kind including its taxonomy, a brief description, and average total length (TL). Though it is possible, even probable, that Crocodylia is a holobaramin, the kind is delineated at the family level because of their strong cognita, interspecific hybridization reported within (but not across) some families, and the need for more understanding of what the molecular data mean.

    1. The Gharial kind—Gavialidae
    Gavialis gangeticus.
    and
    . Tomistoma schlegelii.

    I’m going to continue the discussion on this in the Common Design thread since John apparently doesn’t like discussing the minutia about his own paper once I started highlighting the exact DNA and protein sequences that he himself published in connection with his paper.

    http://theskepticalzone.com/wp/common-design-vs-common-descent/comment-page-97/#comment-205371

  35. Mung:

    So now, when I say that the twin-nested hierarchy is a myth, or when I ask which twin-nested hierarchy, you’ll not have to act all confused, you’ll know exactly what I am talking about.

    The molecular tree matches the morphological tree, except when it doesn’t.

    Why did you change your avatar, Mung? The older one was more appropriate:

  36. newton,

    There are too many assumptions and pressures to keep the universe, but especially our solar system and the earth, as old as possible…
    We should be discussing it elsewhere…
    My apologies to John and the rest…

  37. stcordova:
    Here is diagram highlighting what looks like a parital exon from c-myc from coordinates 355 to 1130 in the TRUE gharial.Since I don’t see the methionine codon (ATG) in this exon, I presume this is not the first exon, further I see the Intron acceptor sequence “ag” just before exon.Further I don’t see the donor site sequence “GT” for the subsequent intron.Do you concur, John?

    What are you trying to do here? If I knew what it was, I might be able to help. What you have may be Gavialis or, given your track record so far, it may not be. But if you read the labels, you would know that you have part of intron 2, all of the coding region of exon 3, and the 3′ untransated region.

    Is the reason we don’t have the whole gene to study, but instead got chopped off like that due to the sequencing technology involved?

    No, it’s due to the fact that we did PCR to amplify a particular region using primers anchored in highly conserved regions.

    You want to discuss the paper don’t you and the data. I mean, this is about the data after all, isn’t it? I’m trying to make sure I got all the data properly referenced to examine.

    All you have to do is find one of the sequences in GenBank, then click on “Popset” to get the entire alignment, which you can conveniently download in FASTA format if you want by clicking another button. Or you could do like the paper says: “The sequence alignment and relevant trees have been uploaded to TreeBase (reference numbers S880 and M1427).”

    I put this sequence in BLASTP for the “False” gharial

    Two problems: first, the protein sequence is not very useful at this level, since as you can see there aren’t many differences among species; second, I don’t vouch for it, as GenBank generates it automatically, though I would have assumed it was OK. Anyway, a detour into protein sequence is pointless, and I advise you not to do that.

  38. stcordova: I’m going to continue the discussion on this in the Common Design thread since John apparently doesn’t like discussing the minutia about his own paper once I started highlighting the exact DNA and protein sequences that he himself published in connection with his paper.

    Don’t be an ass. If you have questions, ask questions rather than posting random long sequences to no apparent purpose.

  39. Mung: So now, when I say that the twin-nested hierarchy is a myth, or when I ask which twin-nested hierarchy, you’ll not have to act all confused, you’ll know exactly what I am talking about.

    The molecular tree matches the morphological tree, except when it doesn’t.

    The point to get out of this is that molecular and morphological trees match almost all the time. Serious conflict is so rare that when it happens, it’s worth publishing. When trees match, not so much.

  40. John Harshman: The point to get out of this is that molecular and morphological trees match almost all the time. Serious conflict is so rare that when it happens, it’s worth publishing. When trees match, not so much.

    So what made your paper worth publishing, did it present a previously unknown topology that conflicted with current molecular phylogenies?

  41. Mung: So what made your paper worth publishing, did it present a previously unknown topology that conflicted with current molecular phylogenies?

    Would it trouble you too much to read at least the introduction? No, it wasn’t previously unknown, and no, it didn’t conflict with current molecular phylogenies. It was however the first nuclear DNA sequence analysis on the subject, and like all previous molecular results, it conflicted with most previous morphological phylogenies.

  42. John Harshman: Would it trouble you too much to read at least the introduction?

    No, not at all. In fact, I even quoted from it earlier in the thread. Do you never ask a question to which you already know the answer?

    You told me that papers that merely confirm what was already known rarely get published. So your paper was, obviously, one of the rare exceptions.

    Congratulations.

  43. It just hit me! Crocodiles didn’t go to the Noah’s Ark, did they? They didn’t have to…
    Sal? Mung?

  44. Mung: You told me that papers that merely confirm what was already known rarely get published. So your paper was, obviously, one of the rare exceptions.

    It isn’t clear to me how you got that from the introduction or from what I said. The conflict was between molecular and morphological data. The paper was the first molecular analysis that, for various reasons, would generally be considered conclusive. But this is all tangential and relatively uninteresting.

  45. Actually this paper makes creationist points.
    First the QUICK FIX idea of convergent evolution to explain likeness that evolutionists use is REJECTED here and hints its used to quickly at best.

    Second. Indeed morphology and genetic scores conflict. important for many reasons.

    anyways.
    Are these crocs more different from each other then human “races” are? i doubt it.
    It shows again that mechanisms that bring body changes are the only thing going on. its not the results that matter.
    SO a kIND in these creatures would include all that had the great number of traits they have. not just a few .
    Crocs probably are not a kind but a type of some other kind that was created on creation week. the fall came and distorted them. They would not of been on the ark and so the diversity would survive better.

    I don’t think genetics does prove a trail. Common design would include common reply to common needs. So its likely they are not sisters any more then with alligators. might be but might not.
    in fact why should evolutionist say convergent evolution couldn’t make convergent genetics while converging?

    a lot of people on one paper.!

  46. J-Mac:
    It just hit me! Crocodiles didn’t go to the Noah’s Ark, did they? They didn’t have to…
    Sal? Mung?

    Yes, the Ark was stocked only with organisms that needed it. Which is why you only see a genetic bottleneck in such species. Except, you don’t.

Leave a Reply